La biopsia liquida. Aldo Scarpa. Anatomia Patologica e ARC-NET Centro di Ricerca Applicata sul Cancro

Transcription

1 La biopsia liquida Aldo Scarpa Anatomia Patologica e ARC-NET Centro di Ricerca Applicata sul Cancro Azienda Ospedaliera Universitaria Integrata di Verona

2 Obstacles to precision oncology Genomic heterogeneity of tumors Emergence of drug resistance Insufficient means for monitoring responses and predict tumor recurrence Collins FS & Varmus H. N Engl J Med. 2015

3 Tumor detection (%) Obstacles to precision oncology Genomic heterogeneity of tumors Emergence of drug resistance Insufficient means for monitoring responses and predict tumor recurrence 100 LONGITUDINAL 80 MONITORING OF DISEASE 20 DYNAMICS 0 Disease monitoring Sensitivity Recurrence Baseline interim Drug X Drug Y

4 One of the Top 10

5 One of the Top 10

6 Liquid biopsy: what is it? cfna Exosomes CTCs

7 Liquid biopsy: what is it? cfna Exosomes CTCs DNA mrna mirna DNA mrna mirna Protein DNA mrna mirna Protein

8 Liquid biopsy: what is it for? Non-invasive access to information through genetics early diagnosis correlation with the burden load minimal residual disease - relapse emergence of drug resistance

9 Liquid biopsy: what is it for? Non-invasive access to information through genetics early diagnosis correlation with the burden load minimal residual disease - relapse emergence of drug resistance It represents a summary of all the different cancer lesions in a patient clonal evolution

10 Liquid biopsy: what is it for? It represents a summary of all the different cancer lesions in a patient Tabassum & Polliack Nat Rev Cancer 2015 clonal evolution

11 Liquid biopsy: cfdna small fragments from apoptotic or necrotic cells has short half-life highly variable level (<0.1% to >50% of total cfdna)

12 Liquid biopsy: cfdna small fragments from apoptotic or necrotic cells has short half-life highly variable level (<0.1% to >50% of total cfdna) Technical challenges: sensitivity and dynamic range

13 Liquid biopsy: cfdna BEAMing (Beads, Emulsions, Amplification, and Magnetics) Droplet digital PCR (ddpcr) Sensitivity < 0.01% Dynamic range > Targeted-NGS Conventional qpcr Sensitivity: up to 0.1%

14 Liquid biopsy: cfdna Early diagnosis applications lack of specificity Newman AM et al. Nature Medicine. 2013

15 Liquid biopsy: cfdna applications Early diagnosis Disease monitoring lack of specificity Newman AM et al. Nature Medicine. 2013

16 Molecular Heterogeneity Lung adenocarcinoma Coexistent EGFR and TP53 mutations Bria et al., Oncotarget 2015

17 Molecular Heterogeneity Lung adenocarcinoma Response to gefitinib of 17 patients with EGFR mutant cancers Analysed for mutations in 20 genes (oncomine solid tumors lifetechnologies) Bria et al., Oncotarget 2015

18 Molecular Heterogeneity Lung adenocarcinoma Response to gefitinib of 17 patients with EGFR mutant cancers * * PMA = Proportion of mutated alleles Bria et al., Oncotarget 2015

19 Lung cancer: cfdna T-NGS EGFR status in tissue and matched cfdna Cas e EGFR status in tissues and matched cfdna FFPE tissue KRAS G12V, TP53 G298* EGFR del KRAS G12C KRAS G12V, TP53 A337C cfdna KRAS G12V, TP53 G298* EGFR del KRAS G12C KRAS G12V TP53 A337C 4 EGFR del EGFR del 5 EGFR del TP53 P190L EGFR del TP53 P190L NGS permits simultaneous analysis of multiple genes and selection of patient specific gene mutation

20 Lung cancer: cfdna ddpcr EGFR status in tissue and matched cfdna EGFR status in tissues and matched cfdna Case Stage ALK FFPE (Pyroseq) cfdna (ddpcr) 1 III - wt wt 2 IV Rearr wt T790M 3 IV - wt T790M 4 III - L858R L858R T790M 5 III - wt wt 6 IV del del 7 IV del del 8 IV del del, T790M 9 IV - wt wt 10 III - wt wt 11 III del del 12 IV - wt T790M 13 IV - wt wt 14 IV - wt T790M 15 IV del del

21 Pancreatic cancer: cfdna Stage II resectable dpcr detected alterations at diagnosis (specificity 99.9%) ctdna detected recurrence before CT Sausen M et al. Nature Communications. 2015

22 Pancreatic cancer: cfdna Stage II resectable dpcr detected alterations at diagnosis (specificity 99.9%) ctdna detected recurrence before CT Sausen M et al. Nature Communications. 2015

23 Colorectal cancer: cfdna Tracking clonal evolution and resistance in the blood Siravegna G et al. Nature Medicine. 2015

24 Liquid biopsy: CTCs Enumeration as prognostic biomarker: CellSearch FDA approved (2004) for prostate and breast cancers Typically <10 cells/ml of blood from a metastatic patient Correlates with tumor burden Aceto N et al. Cell. 2014

25 Liquid biopsy: CTCs Fernandez et al. Breast Cancer Research 2014

26 Liquid biopsy: CTCs Metastatic breast cancer pooled analysis of 17 European Centres PFS OS Bidard F-C et al. Lancet Oncology 2014

27 Liquid biopsy: CTCs CTCs from patients with SCLC are tumorigenic and are representative of the primary SCLC Hodgkinson C et al. Nature medicine. 2015

28 Liquid biopsy: CTCs isolation DEP-Array Silicon Biosystems Fernandez et al. Breast Cancer Research 2014

29 Tumor Burden Pancreatic cancer cellularity Sampl e KRAS Cell KRAS 1 G12R (22%) 15% 60% Keratin Vimentin Fusion

30 Resolving FFPE Intratumoral Heterogeneity Keratin Vimentin Fusion TUMOR STROMAL EMT Recovery of homogeneous pools of cells

31 KRAS TP53 SMAD4 G12R R273H R361H VIM+ KER+

32 KRAS TP53 SMAD4 G12R R273H R361H Stromal Cells VIM+ EMT KER+ Tumor Cells

33

34 Epithelial Ker+ Vim- EMT Ker+ Vim+ Stromal Ker- Vim+ Lymphocyte Ker- Vim-

35 Sundaresan et al. Clin Cancer Res 2015

36 Sundaresan et al. Clin Cancer Res 2015

37

38

39 Introduction in Routine Diagnostics ACCE criteria Analytical validity. degree of accuracy with which a test detects the presence or absence of a mutation Clinical validity. Are the variants the test is intended to identify associated with disease? Clinical utility. clinically useful, or how that risk might be managed ELSI = ethical, legal, and social issues.